diff --git a/internal/engine/runner_integration_test.go b/internal/engine/runner_integration_test.go
new file mode 100644
index 0000000..2c04b05
--- /dev/null
+++ b/internal/engine/runner_integration_test.go
@@ -0,0 +1,342 @@
+package engine
+
+import (
+	"context"
+	"io"
+	"os"
+	"os/exec"
+	"path/filepath"
+	"strings"
+	"testing"
+
+	"github.com/jkleinne/shuttle/internal/config"
+	"github.com/jkleinne/shuttle/internal/log"
+)
+
+// skipIfNoRsync skips the test when rsync is not on PATH, mirroring
+// skipIfNoRclone (rclone_test.go) so the end-to-end suite degrades gracefully
+// on machines without the external tools.
+func skipIfNoRsync(t *testing.T) {
+	t.Helper()
+	if _, err := exec.LookPath("rsync"); err != nil {
+		t.Skip("rsync not found on PATH")
+	}
+}
+
+// seedFile writes dir/name with the given content, failing the test on error.
+func seedFile(t *testing.T, dir, name, content string) {
+	t.Helper()
+	if err := os.WriteFile(filepath.Join(dir, name), []byte(content), 0o644); err != nil {
+		t.Fatalf("seeding %s: %v", name, err)
+	}
+}
+
+// seedDir creates parent/name as a directory holding one file and returns the
+// directory path. rsync receives the source without a trailing slash, so it
+// copies the named directory into the dest, landing files at
+// <dst>/<name>/<file>. A deterministic name keeps that path assertable.
+func seedDir(t *testing.T, parent, name, file, content string) string {
+	t.Helper()
+	dir := filepath.Join(parent, name)
+	if err := os.MkdirAll(dir, 0o755); err != nil {
+		t.Fatalf("creating %s: %v", dir, err)
+	}
+	seedFile(t, dir, file, content)
+	return dir
+}
+
+// rsyncDefaults returns archive-mode defaults. Real configs always set
+// [defaults.rsync] flags; without -a, rsync skips directory sources silently
+// ("skipping directory"), so the copy would never happen and filesystem
+// assertions would be meaningless.
+func rsyncDefaults() *config.Defaults {
+	return &config.Defaults{Rsync: &config.RsyncDefaults{Flags: []string{"-a"}}}
+}
+
+// runPipeline builds a Runner over cfg with a discard logger and a
+// non-interactive ProgressWriter to io.Discard, runs the full pipeline, and
+// returns the Summary. Pass a unique configPath under t.TempDir() so the
+// per-config lock never collides with sibling tests. Fails the test if Run
+// returns an error; scenarios that expect a Run error (lock contention) call
+// NewRunner/Run directly instead.
+func runPipeline(t *testing.T, cfg *config.Config, configPath string, opts RunOptions) Summary {
+	t.Helper()
+	logFile := filepath.Join(t.TempDir(), "test.log")
+	logger, err := log.NewWithWriter(io.Discard, logFile, false, log.VerbosityNormal)
+	if err != nil {
+		t.Fatalf("creating logger: %v", err)
+	}
+	pw := NewProgressWriter(io.Discard, false, false)
+	runner := NewRunner(cfg, configPath, logger, pw, opts.DryRun, logFile)
+	summary, err := runner.Run(context.Background(), opts)
+	if err != nil {
+		t.Fatalf("Run returned error: %v", err)
+	}
+	return summary
+}
+
+func TestPipeline_MultiEngine_AllSucceed(t *testing.T) {
+	skipIfNoRsync(t)
+	skipIfNoRclone(t)
+	cleanup := writeRcloneConfig(t) // sets RCLONE_CONFIG with a [testlocal] local remote
+	defer cleanup()
+
+	rsyncSrc := seedDir(t, t.TempDir(), "data", "local.txt", "local")
+	rsyncDst := t.TempDir()
+
+	rcloneSrc := t.TempDir()
+	seedFile(t, rcloneSrc, "cloud.txt", "cloud")
+	rcloneDst := t.TempDir()
+
+	cfg := &config.Config{
+		Defaults: rsyncDefaults(),
+		Jobs: []config.Job{
+			{
+				Name:        "local-sync",
+				Engine:      config.EngineRsync,
+				Sources:     []string{rsyncSrc},
+				Destination: rsyncDst,
+			},
+			{
+				Name:        "cloud-sync",
+				Engine:      config.EngineRclone,
+				Source:      rcloneSrc,
+				Destination: rcloneDst,
+				Remotes:     []string{"testlocal"},
+				Mode:        config.ModeCopy,
+			},
+		},
+	}
+
+	summary := runPipeline(t, cfg, filepath.Join(t.TempDir(), "config.toml"), RunOptions{})
+
+	if len(summary.Jobs) != 2 {
+		t.Fatalf("len(Jobs) = %d, want 2", len(summary.Jobs))
+	}
+	for _, job := range summary.Jobs {
+		for _, item := range job.Items {
+			if item.Status != StatusOK {
+				t.Errorf("job %q item %q status = %q, want %q", job.Name, item.Name, item.Status, StatusOK)
+			}
+		}
+	}
+	if summary.HasErrors() {
+		t.Errorf("HasErrors() = true, want false (Errors=%v)", summary.Errors)
+	}
+	if len(summary.Errors) != 0 {
+		t.Errorf("Errors = %v, want empty", summary.Errors)
+	}
+	// rsync source has no trailing slash, so "data" is copied into the dest.
+	if _, err := os.Stat(filepath.Join(rsyncDst, "data", "local.txt")); err != nil {
+		t.Errorf("rsync file not at expected path <dst>/data/local.txt: %v", err)
+	}
+	// The runner appends a trailing slash to the rclone local dir source, so its
+	// contents are copied into the dest.
+	if _, err := os.Stat(filepath.Join(rcloneDst, "cloud.txt")); err != nil {
+		t.Errorf("rclone file not at expected path <dst>/cloud.txt: %v", err)
+	}
+}
+
+func TestPipeline_PartialFailure_ContinuesAndRecordsError(t *testing.T) {
+	skipIfNoRsync(t)
+
+	missing := filepath.Join(t.TempDir(), "does-not-exist")
+	healthySrc := seedDir(t, t.TempDir(), "data", "keep.txt", "keep")
+	healthyDst := t.TempDir()
+
+	cfg := &config.Config{
+		Defaults: rsyncDefaults(),
+		Jobs: []config.Job{
+			{Name: "broken", Engine: config.EngineRsync, Sources: []string{missing}, Destination: t.TempDir()},
+			{Name: "healthy", Engine: config.EngineRsync, Sources: []string{healthySrc}, Destination: healthyDst},
+		},
+	}
+
+	summary := runPipeline(t, cfg, filepath.Join(t.TempDir(), "config.toml"), RunOptions{})
+
+	if len(summary.Jobs) != 2 {
+		t.Fatalf("len(Jobs) = %d, want 2", len(summary.Jobs))
+	}
+	// Jobs are dispatched in config order: broken first, healthy second.
+	if got := summary.Jobs[0].Items[0].Status; got != StatusNotFound {
+		t.Errorf("broken status = %q, want %q", got, StatusNotFound)
+	}
+	if got := summary.Jobs[1].Items[0].Status; got != StatusOK {
+		t.Errorf("healthy status = %q, want %q (pipeline must continue past the failure)", got, StatusOK)
+	}
+	if !summary.HasErrors() {
+		t.Error("HasErrors() = false, want true")
+	}
+	if len(summary.Errors) != 1 {
+		t.Fatalf("len(Errors) = %d, want 1 (Errors=%v)", len(summary.Errors), summary.Errors)
+	}
+	if !strings.Contains(summary.Errors[0], "broken") {
+		t.Errorf("Errors[0] = %q, want it to name the 'broken' job", summary.Errors[0])
+	}
+	if _, err := os.Stat(filepath.Join(healthyDst, "data", "keep.txt")); err != nil {
+		t.Errorf("healthy file should have landed: %v", err)
+	}
+}
+
+func TestPipeline_DryRun_WritesNothing(t *testing.T) {
+	skipIfNoRsync(t)
+
+	src := seedDir(t, t.TempDir(), "data", "file.txt", "content")
+	dst := t.TempDir()
+
+	cfg := &config.Config{
+		Defaults: rsyncDefaults(),
+		Jobs: []config.Job{
+			{Name: "dry", Engine: config.EngineRsync, Sources: []string{src}, Destination: dst},
+		},
+	}
+
+	summary := runPipeline(t, cfg, filepath.Join(t.TempDir(), "config.toml"), RunOptions{DryRun: true})
+
+	if !summary.DryRun {
+		t.Error("Summary.DryRun = false, want true")
+	}
+	if got := summary.Jobs[0].Items[0].Status; got != StatusOK {
+		t.Errorf("status = %q, want %q", got, StatusOK)
+	}
+	entries, err := os.ReadDir(dst)
+	if err != nil {
+		t.Fatalf("reading dst: %v", err)
+	}
+	if len(entries) != 0 {
+		t.Errorf("dst not empty after dry-run: %v", entries)
+	}
+}
+
+func TestPipeline_OnlyFilter_SkipsUnselectedJob(t *testing.T) {
+	skipIfNoRsync(t)
+
+	srcA := seedDir(t, t.TempDir(), "data", "a.txt", "a")
+	dstA := t.TempDir()
+
+	srcB := t.TempDir()
+	seedFile(t, srcB, "b.txt", "b")
+	dstB := t.TempDir()
+
+	cfg := &config.Config{
+		Defaults: rsyncDefaults(),
+		Jobs: []config.Job{
+			{Name: "job-a", Engine: config.EngineRsync, Sources: []string{srcA}, Destination: dstA},
+			{Name: "job-b", Engine: config.EngineRsync, Sources: []string{srcB}, Destination: dstB},
+		},
+	}
+
+	summary := runPipeline(t, cfg, filepath.Join(t.TempDir(), "config.toml"), RunOptions{OnlyJobs: []string{"job-a"}})
+
+	if len(summary.Jobs) != 2 {
+		t.Fatalf("len(Jobs) = %d, want 2", len(summary.Jobs))
+	}
+	jobB := summary.Jobs[1]
+	if jobB.Name != "job-b" {
+		t.Fatalf("Jobs[1].Name = %q, want job-b", jobB.Name)
+	}
+	if len(jobB.Items) != 1 || jobB.Items[0].Status != StatusSkipped {
+		t.Errorf("job-b items = %+v, want exactly one StatusSkipped", jobB.Items)
+	}
+	if summary.HasErrors() {
+		t.Errorf("HasErrors() = true, want false (skip is not a failure; Errors=%v)", summary.Errors)
+	}
+	entries, err := os.ReadDir(dstB)
+	if err != nil {
+		t.Fatalf("reading dstB: %v", err)
+	}
+	if len(entries) != 0 {
+		t.Errorf("job-b dest not empty (job-b should have been skipped): %v", entries)
+	}
+	if _, err := os.Stat(filepath.Join(dstA, "data", "a.txt")); err != nil {
+		t.Errorf("job-a file should have landed: %v", err)
+	}
+}
+
+func TestPipeline_LockContention_SecondRunRejected(t *testing.T) {
+	// Empty-jobs config: checkPrerequisites needs no external tool, so this test
+	// runs anywhere. run1 acquires the per-config flock and holds it open
+	// (released only at process exit); a second Run on the same configPath must
+	// be rejected. Calls NewRunner/Run directly rather than via runPipeline,
+	// which would t.Fatalf on the expected error.
+	cfg := &config.Config{}
+	configPath := filepath.Join(t.TempDir(), "config.toml")
+
+	newRunner := func(tag string) *Runner {
+		logFile := filepath.Join(t.TempDir(), tag+".log")
+		logger, err := log.NewWithWriter(io.Discard, logFile, false, log.VerbosityNormal)
+		if err != nil {
+			t.Fatalf("creating logger %s: %v", tag, err)
+		}
+		return NewRunner(cfg, configPath, logger, NewProgressWriter(io.Discard, false, false), false, logFile)
+	}
+
+	run1 := newRunner("run1")
+	if _, err := run1.Run(context.Background(), RunOptions{}); err != nil {
+		t.Fatalf("run1.Run returned error: %v", err)
+	}
+
+	run2 := newRunner("run2")
+	_, err := run2.Run(context.Background(), RunOptions{})
+	if err == nil {
+		t.Fatal("run2.Run returned nil, want a lock-contention error")
+	}
+	if !strings.Contains(err.Error(), "already running") {
+		t.Errorf("error = %q, want it to contain %q", err.Error(), "already running")
+	}
+
+	// Keep run1 alive until after run2 runs so its lock fd is not finalized early.
+	_ = run1
+}
+
+func TestPipeline_RcloneMultiRemote_ExpandsAdjacently(t *testing.T) {
+	skipIfNoRclone(t)
+
+	// Two local-type remotes in a temp rclone config, written inline rather than
+	// extending writeRcloneConfig (which would force its existing testlocal
+	// callers to keep compiling — needless churn for a single test).
+	rcloneConf := filepath.Join(t.TempDir(), "rclone.conf")
+	body := "[testlocal]\ntype = local\n\n[testlocal2]\ntype = local\n"
+	if err := os.WriteFile(rcloneConf, []byte(body), 0o644); err != nil {
+		t.Fatalf("writing rclone config: %v", err)
+	}
+	t.Setenv("RCLONE_CONFIG", rcloneConf)
+
+	src := t.TempDir()
+	seedFile(t, src, "cloud.txt", "cloud")
+	dst := t.TempDir()
+
+	cfg := &config.Config{
+		Jobs: []config.Job{
+			{
+				Name:        "cloud-sync",
+				Engine:      config.EngineRclone,
+				Source:      src,
+				Destination: dst,
+				Remotes:     []string{"testlocal", "testlocal2"},
+				Mode:        config.ModeCopy,
+			},
+		},
+	}
+
+	summary := runPipeline(t, cfg, filepath.Join(t.TempDir(), "config.toml"), RunOptions{})
+
+	if len(summary.Jobs) != 2 {
+		t.Fatalf("len(Jobs) = %d, want 2 (one JobResult per remote)", len(summary.Jobs))
+	}
+	// Both results belong to the same job and are adjacent in remote order.
+	if summary.Jobs[0].Name != "cloud-sync" || summary.Jobs[1].Name != "cloud-sync" {
+		t.Errorf("job names = [%q, %q], want both \"cloud-sync\"", summary.Jobs[0].Name, summary.Jobs[1].Name)
+	}
+	if summary.Jobs[0].Remote != "testlocal" || summary.Jobs[1].Remote != "testlocal2" {
+		t.Errorf("remotes = [%q, %q], want [testlocal, testlocal2]", summary.Jobs[0].Remote, summary.Jobs[1].Remote)
+	}
+	for _, job := range summary.Jobs {
+		if got := job.Items[0].Status; got != StatusOK {
+			t.Errorf("remote %q status = %q, want %q", job.Remote, got, StatusOK)
+		}
+	}
+	if _, err := os.Stat(filepath.Join(dst, "cloud.txt")); err != nil {
+		t.Errorf("rclone file should have landed at <dst>/cloud.txt: %v", err)
+	}
+}